A Survey of Computational Techniques for Genome Sequencing

[1]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[2]  B. Berger,et al.  ARACHNE: a whole-genome shotgun assembler. , 2002, Genome research.

[3]  C. Desmarais,et al.  Automated finishing with autofinish. , 2001, Genome research.

[4]  J. Roach,et al.  Pairwise end sequencing: a unified approach to genomic mapping and sequencing. , 1995, Genomics.

[5]  Eric C. Rouchka,et al.  Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis , 1998, ISMB.

[6]  P. Pevzner,et al.  An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Pavel A. Pevzner,et al.  Towards DNA Sequencing Chips , 1994, MFCS.

[8]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[9]  X. Huang,et al.  An improved sequence assembly program. , 1996, Genomics.

[10]  Mihai Pop,et al.  Genome Sequence Assembly: Algorithms and Issues , 2002, Computer.

[11]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[12]  Dan Gusfield,et al.  Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .

[13]  Esko Ukkonen,et al.  A Greedy Approximation Algorithm for Constructing Shortest Common Superstrings , 1988, Theor. Comput. Sci..

[14]  S. Karlin,et al.  Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[16]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[17]  Jonathan S. Turner,et al.  Approximation Algorithms for the Shortest Common Superstring Problem , 1989, Inf. Comput..

[18]  Eugene W Myers,et al.  On the sequencing and assembly of the human genome , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[19]  S. Kim,et al.  AMASS: A Structured Pattern Matching Approach to Shotgun Sequence Assembly , 1998, J. Comput. Biol..

[20]  X. Huang,et al.  A contig assembly program based on sensitive detection of fragment overlaps. , 1992, Genomics.

[21]  D. Haussler,et al.  Assembly of the working draft of the human genome with GigAssembler. , 2001, Genome research.

[22]  P. Green,et al.  A "quality-first" credo for the Human Genome Project. , 1998, Genome research.

[23]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[24]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[25]  J. Weber,et al.  Human whole-genome shotgun sequencing. , 1997, Genome research.

[26]  Yanggon Kim,et al.  A Fast Multiple String-Pattern Matching Algorithm , 1999 .

[27]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[28]  Michael S. Waterman,et al.  A New Algorithm for DNA Sequence Assembly , 1995, J. Comput. Biol..

[29]  Phil Green,et al.  Whole-genome disassembly , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[30]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Stephanie Forrest,et al.  Genetic algorithms, operators, and DNA fragment assembly , 1995, Machine Learning.

[32]  Eugene W. Myers,et al.  The greedy path-merging algorithm for sequence assembly , 2001, RECOMB.

[33]  Eugene W. Myers,et al.  Combinatorial algorithms for DNA sequence assembly , 1995, Algorithmica.

[34]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[35]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[36]  Li Liao,et al.  A probabilistic approach to sequence assembly validation , 2001, BIOKDD.

[37]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[38]  Nils J. Nilsson,et al.  Artificial Intelligence , 1974, IFIP Congress.

[39]  Owen White,et al.  TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects , 1995 .

[40]  J. Bonfield,et al.  A new DNA sequence assembly program. , 1995, Nucleic acids research.

[41]  Eric S. Lander,et al.  On the sequencing of the human genome , 2002, Proceedings of the National Academy of Sciences of the United States of America.